VMD-L Mailing List

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Aug 31 2006 - 18:02:11 CDT

Hi Cesar,

psfgen will deal with all the info of the psf file. Have a look at
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/7638.html
or follow the example below.

Regards,
Marcos.

vmd protein.psf protein.pdb

set notprot [atomselect top notprot]
package require psfgen

resetpsf
readpsf protein.psf
coordpdb protein.pdb
foreach seg [$notprot get segname] res [$notprot get resid] {
          delatom $seg $res
}

writepsf prot.psf
writepdb prot.pdb

On Thu, 31 Aug 2006, Axel Kohlmeyer wrote:

> On 8/31/06, Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar> wrote:
>> Please help me because I am surely doing something wrong. I am using VMD
>> 1.8.4 under Linux.
>> I load a both psf and pdb files from the shell for a protein in a water
>> box.
>>
>> $ vmd protein.psf protein.pdb
>>
>> I want to remove all the water so now from the tk console I put
>> set prot [atomselect top protein]
>>
>> $prot writepsf prot.psf
>> $prot writepdb prot.pdb
>>
>> Now if I take a look the psf from the shell
>> $ grep angles protein.psf
>> 66246 !NTHETA: angles
>> $ grep angles prot.psf
>> 0 !NTHETA: angles
>>
>>
>> So, the angles have magically disapeared. The same happens to the
>> dihedrals and impropers.
>> Is this a bug or are there some steps that I am missing?
>
> cesar,
>
> this is a 'feature': the psf reader in VMD does not read
> and store the information as it is irrelevant for visualization,
> only the bond information is read.
>
> my guess is, that you might get some help from the
> autopsf tool for what you want.
>
> cheers,
> axel.
>
>>
>> Regards
>> Cesar
>>
>>
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>